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* openPMD-api: 0.11.0+
Upgrade the dependency of openPMD-api to 0.11.0 or newer.
This version has all defaults for independent I/O with HDF5,
ADIOS1 (and as before in ADIOS2) in place.
* openPMD-api: use new setSoftwareVersion
Use new, less error-prune API call to document the WarpX
software version.
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* Initial work to add back QED particle generation
* Work in progress: port old QED routines
* Add two distinct CopyFuncs
* modified getMFItInfo and CopyFunc (not working)
* bugfixing & work to add back QED particle creation routines
* bugfixing
* added back quantum photon emission
* bugfixing
* bugfixing
* added back pair generation (still some bugs in photon emission)
* removed unwanted check
* bugfixing
* bugfixing
* bugfixing
* Moved QED folder
* added comments + some refactoring
* added comments
* remove some virtual functions to make lgtm happy
* updated tests
* added PhysicalParticleType
* bugfixing
* added copyright
* improved comments
* improved comments
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* moved inclusion of QEDInternals folder
* moved some inclusion directives between Make files
* moved some inclusion directives between Make files (forgot to add a file)
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* corrected alignment
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* removed some unnecessary amrex::
* add missing comment
* Replaced BL_PROFILE with WARPX_PROFILE
* bugfixing and making some variables const
* removed some moves
* removed some moves
* started to change tau into optical_depth_BW or optical_depth_QSR
* Using initialization policy to initialize optical depth
* bugfixing
* forgot to add a file
* fixed bug
* Revert "fixed bug"
This reverts commit a3fb98d10cc30327635aeaa71451a05ca2229ff4.
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Added doQEDEvents to OneStep_sub1
* add a bunch of const
* add _rt suffix
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* added path to included files
* Introduced a templated AmIA<something> function using physical_species
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* added paths to included headers
* updated documentation
* updated examples
* bugfixing
* bugfixing
* fixing examples
* fixed example
* fixed example
* correct a misprint in error message
* fixed issue related to 1./mass for photons
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* make the use of energy_threshold more transparent
* remove unnecessary checks
* bigfixing
* added comment
* separate checks for QED processes
* added a CheckIonizationProductSpecies for consistency
* bugfixing
* now using a new variable for photon energy creation threshold
* removed unwanted comment
* added option to set a user-defined threshold for photon creation
* bugfixing
* updated documentation
* updated example to include new option
* updated doc
* fixed merge conflict
* correct bug in example
* reorganized function
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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* added new function WarpXUtilMsg::AlwaysAssert
* Update Source/Utils/WarpXUtil.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Utils/WarpXUtil.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* rename argument of AlwaysAssert
* updated documentation of Always Assert
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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(#772)
* For RZ, generalized the centering of the inverse volume scaling of J and rho
* Add assert ensuring that Jr is never node-centered
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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* Prepare EvolveE
* Cartesian equations without current
* Implement Cartesian EvolveE
* Progress towards cylindrical solver
* Correct typo
* Implement cylindrical solver (without on-axis condition)
* Fix compilation errors
* Add regularization for RZ solver
* Added correction term for F
* Remove file for nodal stencil
* Apply stylistic changes to EvolveE
* Fix compilation errors
* Correction to avoid out of bound
* Remove references to old file
* Correct bug in EvolveB
* Implement correction on axis for Et
* Remove previous field update functions
* Implement EvolveF in Cartesian
* Add missing file
* Update on-axis condition
* Correct typo
* Add theta derivative for divE calculation
* Fix rho component
* Fix compilation error
* Use C++ templates in computation of divE
* Update Source/FieldSolver/FiniteDifferenceSolver/ComputeDivE.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Apply suggestions from code review
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Use comparisons to 0 again
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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* Add Histogram
* Add normalization
* Add doc
* Minor
* Minor
* Fix a bug
* Add const
* Apply suggestions from code review
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Modify based on suggestions.
* Add histogram name
* Add bin values
* Don't add histogram name
* Modify read_raw_data.py
* Add doc
* Change ux,uy,uz units
* Change ux,uy,uz units
* Change if format
* Save some variables
* Change more
* Minor
* Fix a bug on GPU
* Fix a bug on GPU
* Add wrong species name abort
* Minor doc
* Change #include format
* Apply suggestions from code review
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Add const
* Change to member variables
* revert
* Modify doc
* Change ReduceRealSum
* Improve by using enum
* Remove no_normalization
* Add struct
* Minor format
* Apply suggestions from code review
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Change based on suggestions
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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functions should run. (#803)
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* fix compilation for single precision PSATD with USE_GPU
* compiles and tested on CPU also
* add sentence to doc: FFTW needs to be compiled with single precision option
* add test, better pre-proc directives indent, clearer ifdef
* use using whenever possible
* indent
* fix TravisCI matrix, and improve matrix test
* need to compile with same precision for fields and particles
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* For diagnostics, added RZ modes of scalars, allowed different centerings
* Fixed spacing in ConstructTotalRZScalarField
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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* Added abort error for insufficient #cells in phi
* Fixed language in error message
* Added #parts per theta limit in docs
* Fixed initialization of n_rz_azimuthal_modes
* Fixed abort message cpp errors
* Fix n_rz_azimuthal_modes read from WarpX class
* Fix wrong index in num_particles_per_cell_each_dim
* Fix PR# and abort message without additional variable
* Fixed LWFA RZ example
* Changed Abort to AssertWithMessage
* Corrected inequality to include case of x2
* RZ #modes=1 by default. Fix #parts in theta =2
* Fix to LWFA RZ #modes=2 #parts in theta=4
* Added limitation in #parts in theta for NRandomPerCell style
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* Changed BL_ASSERT to AMREX_ALWAYS_ASSERT for user input
* Fixed typo when replacing BL_ASSERTs
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* added error message if laser amplitude is not positive
* moved assert to LaserParticleContainer
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(#787)
* Added optional user defined number of quard cells to use with PSATD solver.
* Removed temporary comments.
* Changed names nx_guard_psatd to psatd.nx_guard for consistency.
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For single precision, roughly 4-5 significant digits are comparable
for our floating point precision tolerance.
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* Include private members of classes in Doxygen documentation
* add space before bracket for function implementation
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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* Allowed for more general centering of charge density
* Used rho_nodal_flag in ApplyInverseVolumeScalingToChargeDensity
* Simplify declaration of rho_nodal_flag
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Fix documentation for doChargeDepositionShapeN
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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* Create inputs
* fixed stuff
* Make smaller test
* Re-use EvolveEM for ES calculation
* Use correct variable const_dt
* Avoid out of bound and modify computation of electrostatic field
* Update test file
* Remove tab
* Minor refactoring of space-charge calculation
* Remove old electrostatic files
* Fix electrostatic test
* Rename WarpXEvolveEM to WarpXEvolve
* Use if conditions instead of ifdef
* Correct initialization of `do_electrostatic`
* Fix static variable
* Add documentation for `do_electrostatic`
* Remove more electrostatic code
Co-authored-by: dbizzozero <dbizzozero@users.noreply.github.com>
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update (#773)
* Add default prtl and cell wts for costs update
Remove print
Cleanup
Typo
* Add AMREX_USE_GPU ifdef
* Add default costs for CPU case
* Formatting
* Add comment that default values are for Summit
* Explain tests in doc
* Formatting
* Clarify logic
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* Create inputs
* fixed stuff
* Make smaller test
* Re-use EvolveEM for ES calculation
* Use correct variable const_dt
* Avoid out of bound and modify computation of electrostatic field
* Update test file
* Remove tab
* Minor refactoring of space-charge calculation
* Fix electrostatic test
* Rename WarpXEvolveEM to WarpXEvolve
* Use if conditions instead of ifdef
* Correct initialization of `do_electrostatic`
* Fix static variable
* Add documentation for `do_electrostatic`
Co-authored-by: dbizzozero <dbizzozero@users.noreply.github.com>
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* Fix compilation for hybrid PSATD
* Add automated test for hybrid PSATD
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* corrected two typos missed during review of PR-719
* changed file permission from executable to read/write
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* first implementation, doesnt link
* fix species type and use it in some examples
* eol
* typo in input file
* Apply suggestions from code review
Co-Authored-By: Luca Fedeli <luca.fedeli.88@gmail.com>
Co-Authored-By: Yinjian Zhao <yinjianzhao@lbl.gov>
* changes suggested by review
* put species functions into a namespace
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
Co-authored-by: Yinjian Zhao <yinjianzhao@lbl.gov>
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* Issue #713: Load Balance w.r.t. number of cells + particles
README: Update Badged to `master` (#725)
* README: Update Badged to `master`
Update the badges to check the `master` branch as development branch.
* Docs: More dev->master updates
- release workflow
- contribution guide link
Galilean PSATD with shift (#704)
* Read Galilean velocity
* Prepare structures for Galilean solver
* Started implementing Galilean equations
* Analytical limits for X1, X2, X3, X4 coefficients added
* Slight changes added
* Added Galilean position pusher
* Scale galilean velocity
* Remove unneeded Abort
* Fix Galilean pusher
* Allocate Theta2 array
* Fix definition of coefficients
* Increase guard cells for Galilean
* Add guard cell in particle exchange
* Type corrected
* v_gal added to warpx_current_deposition
* v_gal added to WarpXParticleContainer.H
* Bug fixed - update particle x-position over one time step
* Fix issues with merge from dev
* Preparation for merging dev into galilean.
* Adding galilean shift
* Implemented galilean shift
* Changed method's name from GalileanShift to ShiftGalileanBoundary
* Added doxygen string for ShiftGalileanBoundary
* Removed never used method LowerCornerWithCentering
* Removed temporary comments
* Removed dt as a variable from DepositCharge method and its dependencies
* Converted tab to spaces
* Removed EOL white space
* Add documentation and automated tests
* Fix compilation error
* Add automated test
* Update automated test
* Removed temporary used galilean shift
* Removed temporary used particle's push for Galilean PSATD
* Removed unused statement
* Remove EOL white space.
* Added zero shift for LowerCorner in RZ geometry
* Minor changes to Galilean implementation
* Modifications for GPU
* Fix typo
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
[mini-PR] when a cufft error occurs, print a meaningful error message (#728)
* added method to translate cufft errors
* fixed style
* bug fixing
avoid duplicate tests and plot less often (#726)
* avoid duplicate tests and plot less often
* fix tests I broke when trying to save plotfiles
doc install yt on Summit (#729)
* doc install yt on Summit
* eol
Do not use local Redistribute for electrostatic solver (#731)
Add Reset Random Seed Feature (#717)
* Add ResetRandomSeed
* Add doc
* Modify and change location of the code.
* Small fix
* Try to fix an alert
* Try to fix an alert
* Modify based on suggestions
* Use INT_MAX
* Modify based on suggestions.
* Modify based on suggestions.
openPMD: warn if step is already written (#718)
* making sure iterations are written at most once.
* prints a warning when iteration is written more than once
writting is not stopped
* Fixed tabs
* included <iostream> as requested by Axel
Minor refactoring of space-charge calculation (#732)
Improve clarity and documentation
Minor
Update GNUmakefile
Update based on comments
Update GNU Makefile
Formatting
Formatting
Formatting
Formatting
Remove unneeded function
Removed unneeded function
Formatting
Formatting
Formatting
Whitespace
Minor
Formatting
Formatting
Formatting
Formatting
Formatting
Formatting
Formatting
whitespace
Formatting
Minor
Formatting
Remove unneeded template function
Change import
Minor
Formatting
Remove unused variable
Formatting
Update Source/WarpX.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
Update Source/Parallelization/WarpXRegrid.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
Remove `n_particles` and `n_cells`
Update Source/WarpX.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
Revert clear costs in case of edge case
Update to use new load_balance_api in AMReX
Tabs
Minor
* minor: indentation in Source/WarpX.H
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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Generalize includes to base path.
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* replace tau by optical_depth_QSR and optical_depth_BW
* update python analysis scripts accordingly
* fix bug for BW
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* avoid using namespace amrex in .H files
* need amrex prefix to function arguments
* typo
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* add acknowledgement doc section
* better phrasing and fix citation
* typo
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Use the `clang-tidy` pass `misc-unused-parameters` to remove unused
parameter warnings.
https://clang.llvm.org/extra/clang-tidy/checks/misc-unused-parameters.html)
Committed as generic user so git does not credit the many lines to me:
```bash
GIT_AUTHOR_NAME="Tools" GIT_AUTHOR_EMAIL="warpx@lbl.gov" \
git commit
```
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* Implement div(E) diagnostics for spectral case.
* split travis tests in bigger matrix
* split more TravisCI tests, add electrostatic, use defaults values
* typo
* Move computation of div(E) to base class SpectralBaseAlgorithm.
* need to split psatd too
* consistent variable names and use function to avoid duplication
* fix typo for qed tests
* typo
* also need to update run_tests.sg
* Update copyright tags.
* change matrix
* Add test of div(E) vs rho/epsilon_0 in PML test.
* SpectralFieldIndex: reuse memory slot for Bx when computing divE.
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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* clarify that we WANT PRs to be small
* Update CONTRIBUTING.md
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Defining a variable-length array (VLA) is a C99 feature.
It's conditional in C11 and actually not part of C++ either :)
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* Prepare EvolveE
* Cartesian equations without current
* Implement Cartesian EvolveE
* Progress towards cylindrical solver
* Correct typo
* Implement cylindrical solver (without on-axis condition)
* Fix compilation errors
* Add regularization for RZ solver
* Added correction term for F
* Remove file for nodal stencil
* Apply stylistic changes to EvolveE
* Fix compilation errors
* Correction to avoid out of bound
* Remove references to old file
* Correct bug in EvolveB
* Implement correction on axis for Et
* Remove previous field update functions
* Remove unused code
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Fix type conversions when compiling with `PRECISION=FLOAT`.
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Add `.SP` for `PRECISION=FLOAT` and `.pSP` for
`USE_SINGLE_PRECISION_PARTICLES=TRUE` as binary suffix.
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